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1,582 results for “manuscript”

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zenodo44/100

Processed data for the manuscript, entitled "Substantial increase in heavy precipitation events preceded by moist heatwaves over China during 1961–2019"

<p>This is the dataset on annual frequency of heatwaves, heavy precipitation, and heatwave-heavy precipitation events during 1961-2019 at 1776 stations across China. This dataset is the processed results based on daily observations that are provided by&nbsp;the National Meteorological Science Data Center (<a href="http://data.cma.cn/en">http://data.cma.cn/en</a>). In this processed dataset, the &quot;HW_HI&quot; column is the annual frequency of heat-index-based heatwaves; &quot;HW_TW&quot; column is the annual frequency of&nbsp;wet-bulb temperature based heatwaves; &quot;HP&quot; is the annual frequency of heavy precipitation with taking&nbsp;the 95<sup>th</sup> percentile of non-zero precipitation at the threshold. &quot;HWHP_HI&quot;/&quot;HWHP_TW&quot; column indicate annual frequency of heavy precipitation preceded by HW_HI/HW_TW. All the results shown in the manuscript entitled &quot;<strong>Substantial increase in heavy precipitation events preceded by moist heatwaves over China during 1961</strong>&ndash;<strong>2019</strong>&quot;, are obtained based on this processed dataset.</p>

opencc-by-4.0Aug 2021View details →
zenodo44/100

Dataset and Code for Manuscript "Multi-angle pulse shape detection of scattered light in flow cytometry for label-free cell cycle classification"

<p>Dataset of measurements for cell cycle analysis with description:</p> <ul> <li>ReadMe file with explanations on the data set and analysis</li> <li>exemplary Matlab script file for analysis</li> <li>binary data files conatining the pulse shapes in all channels</li> <li>FCS data files containing common flow cytometry parameters in each channel</li> </ul> <p>Data on unsorted HEK cells, HEK cells sorted for cell cycle phases, and unsorted Jurkat cell are included.</p>

opencc-by-4.0Aug 2021View details →
zenodo44/100

Data and code associated with manuscript by Gibert et al

<p>This is the code and data associated with the article :&quot;Non-reproducible signals of adaptation to elevation between light and shade environments in Snapdragon plants&quot; by Gibert et al published in Journal of Evolutionary Biology</p>

opencc-by-4.0Sep 2021View details →
zenodo44/100

Dataset for the manuscript "Are remote sensing evapotranspiration models reliable 2 across South American ecoregions?" published in WRR

<p><strong>Metadata of &lsquo;<em>Are remote sensing evapotranspiration models reliable across South American ecoregions?</em>&rsquo; &nbsp;</strong></p> <p>This document describes the file formatting and data used to run and evaluate the evapotranspiration models in this study. Because forcing data varies among models, each input file contains a different set of meteorological data&nbsp;placed within a folder named after the corresponding model.</p> <p>&nbsp;</p> <p><strong>File format and time stamps</strong></p> <p>Data files are CSV formatted with timestamps in the first column of the file. The following timestamps are used:</p> <ul> <li>GLEAM: Year (YYYY); Day of Year (DDD)</li> <li>PT-JPL: Year (YYYY); Month (MM); Day (DD)</li> <li>PM-MOD: Year (YYYY); Month (MM); Day (DD)</li> <li>PM-VI: Date (MM/DD/YYYY)</li> </ul> <p>&nbsp;</p> <p><strong>Missing data</strong></p> <p>Missing data are reported using &lsquo;NaN&rsquo; as a replacement flag. Data for all days in a leap year are reported.&nbsp;</p> <p>&nbsp;</p> <p><strong>Data format</strong></p> <p>The column headers Name, Description and Units&nbsp;are adopted used in the data files to describe the following variables::</p> <ul> <li>ETo,&nbsp;Penman-Monteith FAO-56 reference evapotranspiration (mm day<sup>-1</sup>);</li> <li>ETobs, Observed evapotranspiration (mm day<sup>-1</sup>);</li> <li>Rn, Surface Net Radiation (w m<sup>-2</sup>);</li> <li>Rg, Daylight shortwave Incoming Radiation (w m<sup>-2</sup>);</li> <li>Rgs_out, Shortwave Radiation -&nbsp;outgoing (w m<sup>-2</sup>);</li> <li>G, Soil heat flux (w m<sup>-2</sup>);</li> <li>P,&nbsp;Rainfall (mm day<sup>-1</sup>);</li> <li>T, Surface Air Temperature (&ordm;C);</li> <li>Tmax,&nbsp;Maximum Temperature (&ordm;C);</li> <li>Tmin, Minimum Temperature (&ordm;C);</li> <li>Tday, Daytime Temperature (&ordm;C);</li> <li>TminDay, Daytime Minimum Temperature (&ordm;C);</li> <li>TminNight, Nighttime Minimum Temperature (&ordm;C);</li> <li>Patm, Atmospheric Air Pressure (Pa);</li> <li>ea,&nbsp;Actual Vapor Pressure (kPa);</li> <li>es, Saturation Vapor Pressure (kPa);</li> <li>VPD,&nbsp;Vapor Pressure Deficit (kPa);</li> <li>eaDay, Daytime Actual Vapor Pressure (kPa);</li> <li>eaNight, Nighttime Actual Vapor Pressure (kPa);</li> <li>RH, Air Relative Humidity;</li> <li>RHDayTime, Daytime Air Relative Humidity;</li> <li>RHNightTime, Nighttime Air Relative Humidity;</li> <li>LAI, Leaf Area Index (m&sup2; m<sup>-</sup>&sup2;);</li> <li>SWC, Soil Water Content (mm m<sup>-1</sup>).</li> </ul> <p>&nbsp;</p> <p><strong>Forcing data per model</strong></p> <p>Each model requires a different set of forcing data, as follows:</p> <ul> <li>GLEAM: Rn, P, T, Rgs_out;</li> <li>PT-JPL: Tmax, Rn, RH (or e<sub>a</sub>);</li> <li>PM-MOD: Rg, Tday, TminDay, TminNight, RHDayTime, RHNighttime, eaDay, eaNight;</li> <li>PM-VI: ETo.</li> </ul> <p>&nbsp;</p> <p><strong>Tower sites (IDs)&nbsp;and co-authors/PIs:</strong></p> <ul> <li>SDF: J. P. Quezada and&nbsp;M.&nbsp;Galleguillos;</li> <li>TF1 and TF2: L. Kutzbach and&nbsp;D.&nbsp;Holl;</li> <li>GRO and SLU: G.&nbsp;Posse;</li> <li>BAL and MCC: M. Gassman and&nbsp;C.&nbsp;Perez;</li> <li>PDG, EUC and USR: O.&nbsp;Cabral;</li> <li>FM and SIN: J.S. Nogueira and&nbsp;T. Range;</li> <li>CAA: M. Moura;</li> <li>CST: A. C. D. Antonino;</li> <li>SJO: E. S. Souza and&nbsp;J. R. S. Lima;</li> <li>ESEC:&nbsp;B. Bezerra.</li> </ul>

opencc-by-4.0Oct 2021View details →
zenodo44/100

Ouseley mission to Persia 1810-15 – Data on oriental manuscripts collected by the Ouseley brothers

<p>These files form part of an archive of research data relating to the diplomatic mission to Persia 1810-15, led by Sir Gore Ouseley as ambassador. The data have been compiled by independent researchers W H (Bill) Martin and Sandra Mason;&nbsp; their contact details are in the README file..&nbsp; The files comprise a number of searchable listings relating to the reports produced by members of the mission and other relevant data.&nbsp; The data formed the basis for a published report on the Ouseley Mission referenced below, which is also part of the archive.&nbsp;</p> <p>This section of the archive contains three databases, under the general heading of <em>ouscollect</em>, listing the main items in the Ouseley collections of oriental manuscripts now held at the Bodleian Library in Oxford.&nbsp; Some of these items were undoubtedly acquired during the Ouseley mission to Persia 1810-15.&nbsp; Other were obtained during the brothers earlier stays in India or through booksellers in London and elsewhere.&nbsp;&nbsp;The database files have been saved in two formats:&nbsp; a Microsoft Access database (<em>ouscollect.accdb</em>) covering all the Ouseley holdings, and three separated comma-delimited text files (<em>.txt</em>).&nbsp; The&nbsp;explanatory README text file contains a table showing the fields included in the databases and giving definitions of them and of the codings used in different cases.&nbsp;</p>

opencc-by-4.0Dec 2018View details →
zenodo44/100

Data for the "Does prognostic seeding along flight tracks produce the desired effects of cirrus cloud thinning?" manuscript

<p>Tar file of the data used to prepare the plots and write the text in: &quot;Does prognostic seeding along flight tracks produce the desired effects of cirrus cloud thinning?&quot; manuscript for submission to ACP.</p> <p>A description of each netcdf file is provided in the README file. The format of each file is in netcdf4</p>

opencc-by-4.0Nov 2022View details →
zenodo44/100

Supporting data for the manuscript: "The Role of Mesoscale Cloud Morphology in the Shortwave Cloud Feedback"

<p>This repository contains supporting data for the manuscript &quot;The Role of Mesoscale Cloud Morphology in the Shortwave Cloud Feedback&quot; in <em>Geophysical Research Letters</em>. Detailed descriptions of these datasets can be found in the manuscript text as well as in the file descriptions.</p>

opencc-by-4.0Nov 2022View details →
zenodo44/100

Data base for the known manuscripts that transmit the chronicle of Jakob Twinger von Königshofen

<p>The database derives from my research for my PhD, which I conducted between 2013 and 2017 at the University of Freiburg (Germany). The thesis was defended in summer 2018 and published in 2020 with De Gruyter: <a href="https://doi.org/10.1515/9783110636475">Ina Serif: Geschichte aus der Stadt. &Uuml;berlieferung und Aneignungsformen der deutschen Chronik Jakob Twingers von K&ouml;nigshofen. Berlin/Boston 2020</a>. I have been using <a href="https://nodegoat.net/">nodegoat</a> for several years now as my working and data storing environment. As it is a relational database, the export for this repository consists of two files: the main file, manuscripts.csv, which contains the manuscripts and their metadata, and a content file, content.csv, which contains the relations between texts and manuscripts, using &quot;nodegoat_ID&quot; as identifier. As of 2022, the main file consists of 128 records, the content file of 1220 entries. You should be able to import it to the software you prefer, linking the content to the manuscripts through &quot;nodegoat_ID&quot;. The metadata fields for the manuscripts are the following: nodegoat ID, Institution, Call no., Sigle, Folio no., Material, Language, illustrated, Exact date of origin, Date of origin, Place of origin, Place certain, Chronicle Version, Additional info. The information about the single codices derives from manuscript catalogues, research articles, and own analyses. For a complete bibliography of the used literature see my thesis, pp. 215&ndash;245. As this is a finished research project, the database gets updated only on an irregular basis. I am also maintaining an online article about the known manuscripts and existing digital versions: Ina Serif: Der zerstreute Chronist. Zur &Uuml;berlieferung der deutschsprachigen Chronik Jakob Twingers von K&ouml;nigshofen, in: Mittelalter. Interdisziplin&auml;re Forschung und Rezeptionsgeschichte, 2/2015, last update 10/2021, <a href="https://mittelalter.hypotheses.org/7063">https://mittelalter.hypotheses.org/7063</a>. The record for the chronicle in the <a href="https://handschriftencensus.de/werke/1906">Handschriftencensus</a> does not list all manuscripts that I consider to be textual witnesses (as of October 2021, it lists 115 manuscripts), but contains additional information regarding single codices.</p>

opencc-by-4.0Dec 2022View details →
zenodo44/100

The e-NDP project : collaborative digital edition of the Chapter registers of Notre-Dame of Paris (1326-1504). Ground-truth for handwriting text recognition (HTR) on late medieval manuscripts.

<p>The <a href="https://endp.hypotheses.org/">e-NDP project</a>, funded by the ANR, is led by the <a href="https://lamop.hypotheses.org/6870">LaMOP</a> (Julie Claustre and Darwin Smith).</p> <p>The project&#39;s partners are the Archives nationales, the&nbsp;Biblioth&egrave;que nationale de France (Department of Manuscripts, Biblioth&egrave;que de l&#39;Arsenal), the &Eacute;cole nationale des chartes and the Biblioth&egrave;que Mazarine.</p> <p>The e-NDP project aims at renewing our knowledge on <strong>Notre-Dame de Paris cathedral</strong> through the creation of a collaborative digital edition of the registers of its Chapter (1326-1504, <em>AN LL 105-128</em>), the community of 51 canons meeting three times a week on set days to take all administrative, financial and practical decisions pertaining to the cathedral, its estate and the society living in its cloister. This corpus has never been the object of a comprehensive study to understand the workings and history of this urban enclave and powerful community. The collaborative digital edition is based on a process of<strong> handwriting text recognition (HTR)</strong>, tested and supervised by scholars, researchers and engineers combining expertise in Medieval history, paleography, philology and digital humanities. The edition shall allow a better insight into the Chapter&rsquo;s administration, into its economical and political power within Paris, and the relationships it maintained with other institutions in the city.</p> <p>&nbsp;</p> <p><strong>Section 1 : The e-NDP ground-truth dataset for Handwriting text recognition.</strong></p> <p>The full e-NDP corpus kept today in the French National Archives and was entirely digitized and described in its&nbsp;<a href="https://www.siv.archives-nationales.culture.gouv.fr/siv/rechercheconsultation/consultation/ir/consultationIR.action?formCaller=GENERALISTE&amp;irId=FRAN_IR_059635">catalog</a>&nbsp;in 2022.</p> <p>The first major goal of the&nbsp;e-NDP projet is to propose a first automatic transcription of the 14k pages composing the 26 chapter registers. To achieve this goal representative samples from&nbsp;each one of the volumes were selected and transcribed in order to train a specialized HTR model able to propose a high quality automatic transcription. The collected ground-truth released on this repository currently has <strong>512 pages from the 26 registers</strong> of the cathedral chapter preserved in the National Archives (LL105 - LL128, <strong>1326-1504</strong>). The transcriptions were manually completed in <strong>two rounds</strong> by a group of 12 contributors, historians and paleographers, over the course of 2021-2022 using <a href="https://escriptorium.paris.inria.fr/">eScriptorium </a>as annotation environment.&nbsp;&nbsp;</p> <p>&nbsp;</p> <p><strong>Ground-truth features :</strong></p> <p><br> <em>Number of hands </em>: according to our estimates no fewer than 18&nbsp;main hands were involved in the writing of the registers during the medieval period.&nbsp;</p> <p><em>Language</em> : More than 98% of the content of the registers was written in Latin, the rest in French. The exact percentage is hard to estimate because the vernacular language is often used in formulae, notes and comments. It is rare to find entire pages or blocks written in French.&nbsp;</p> <p><em>Script family</em> : The registers were written using a Cursive script (ca. late XIIIe - XVIe).</p> <p><em>Documental typology</em> : The volumes containing the chapter conclusions were conceived to serve&nbsp;as memorial&nbsp;records, but above all as documents for regular use and consultation in the daily practice of administration and management. In diplomatics the notion of &quot;documentary manuscripts&quot; is used to describe this kind of sources&nbsp;also by opposition to books and litterary or&nbsp;normative&nbsp;manuscripts.</p> <table align="center"> <caption><strong>Ground truth statistics</strong></caption> <tbody> <tr> <th>Text units</th> <th>Count</th> </tr> <tr> <td>Pages</td> <td>512</td> </tr> <tr> <td>Annotated regions (see section 2)</td> <td>2448</td> </tr> <tr> <td>Lines of text</td> <td>34231</td> </tr> <tr> <td>Tokens</td> <td>205083</td> </tr> <tr> <td>Characters</td> <td>3320407</td> </tr> </tbody> </table> <p>&nbsp;</p> <p><strong>Rules of transcription :</strong></p> <ul> <li>The abbreviations have been resolved, both those by suspension (<code>facimꝰ</code> ---&gt; <code>facimus</code>) and by contraction (<code>d&ntilde;i</code> --&gt; <code>domini</code>). Likewise, those using conventional signs (<code>⁊</code> --&gt; <code>et</code> ; <code>ꝓ</code> --&gt; <code>pro</code>) have been resolved.&nbsp;</li> <li>The named entities (names of persons, places and institutions) have been <code>capitalized</code>. The beginning of a block of text as well as the original capitals used by the notary are also capitalized.</li> <li>The consonantal <code>i</code> and <code>u</code> characters have been transcribed as <code>j</code> and <code>v</code> in both French and Latin.</li> <li>The punctuation marks used in the text: <code>.</code> and <code>/</code> have been transcribed, but the transcription has not been standardized with modern punctuation.</li> <li>Corrections and words that appear cancelled in the manuscript have been transcribed surrounded by the sign <code>$</code> at the beginning and at the end.</li> <li>More specific transcription rules can be found into the file <code>transcription_guidelines.pdf</code></li> </ul> <p>&nbsp;</p> <p><strong>Section 2. e-NDP Layout Segmentation.</strong></p> <p>Layout segmentation is a compulsory step before HTR recognition in order to distinguish sections and regions inside a document. This process intend to separate interdependant page zones to produce a recognition in a section-sequence order and not in a line-sequence order which mix textual and peri-textual content.</p> <p>The regions of 364&nbsp;pages (see <code>GT-layout_list</code>) of the e-NDP corpus were annotated using a 5 sections vocabulary (see <code>endp_layout_regions</code>) in order to describe&nbsp;the page distribution in all the 26 volumes :</p> <ol> <li><em>Block</em>&nbsp;: All the central text blocks, that normally corresponds to the main content called &quot;conclusions&quot; in registers.</li> <li><em>Liste</em>&nbsp;: List of names of the canons who were present during the meeting. Normally located before the <em>conclusions</em>.</li> <li><em>Entr&eacute;e</em>&nbsp;: Marginal notes or entries to inform about the content of <em>conclusions</em>.</li> <li><em>Date</em>&nbsp;: Paragraph contending the date. Normally at the head of a <em>conclusion</em>, but separate of the main body.</li> <li><em>Num&eacute;rotation</em>&nbsp;: Page numbers in roman or arabic. Usually appear in the top corners of the pages.</li> </ol> <table align="center"> <caption><strong>Layout GT statistics</strong></caption> <tbody> <tr> <th>Region</th> <th>Count</th> </tr> <tr> <td>block</td> <td>833</td> </tr> <tr> <td>liste</td> <td>431</td> </tr> <tr> <td>date</td> <td>448</td> </tr> <tr> <td>entr&eacute;e</td> <td>205</td> </tr> <tr> <td>num&eacute;rotation</td> <td>531</td> </tr> </tbody> </table> <p>&nbsp;</p> <p><strong>Section 3. The e-NDP HTR modeling.</strong></p> <p>The e-NDP project has progressively trained several HTR models adapted to work on late medieval cursive in order to accelerate the production of ground truth. Currently the best model delivers an average&nbsp;<strong>CER (Character error ratio) of 9.7%</strong> in handwriting recognition on&nbsp;the 26 registers (see <code>endp_learning_curve</code>) and can serve as generalist model&nbsp;for other manuscripts of the same period and similar script family. These models and their training implementation details can be found in the project&#39;s github <a href="https://github.com/chartes/e-NDP_HTR">repository</a>.&nbsp;</p> <p>Additionally, the automatic HTR transcriptions of the 26 registers (14k pages, 4.5M tokens) enriched with lexical and semantical information has been the subject of a first <a href="https://nosketch-engine.lamop.fr/#dashboard?corpname=endp">online publication</a> using the NoSketch engine that allows advanced data mining based on the combination of data, metadata and NLP features.&nbsp;</p> <p>&nbsp;</p> <p><strong>Section 4. Dataset content.</strong></p> <p>This zip dataset contains :</p> <p>- <code>HTR_ground_truth</code> : Two folders containing the jpg / jpeg images and their curated transcriptions in PAGE XML format.</p> <p>- <code>images_docs</code> : 4 files illustrating the different phases of the project (list of GT for layout segmentation, layout ontologie, transcription guideline and HTR evaluation curves)</p>

opencc-by-4.0Feb 2023View details →
zenodo44/100

Dataset to the manuscript "Deciduous tundra shrubs shift toward more acquisitive light absorption strategy under climate change treatments"

<p>The three datasets were used for the statistical analysis for the manuscript entitled &quot;Deciduous tundra shrubs shift toward more acquisitive light absorption strategy under climate change treatments&quot;.</p>

opencc-by-4.0Dec 2022View details →
zenodo44/100

Dataset for manuscript: Rock anisotropy promotes hydraulic fracture containment at depth

<p>This is the&nbsp;experimental data&nbsp;used in manuscript: &quot;Rock anisotropy promotes hydraulic fracture containment at depth&quot;.</p> <p>This data set has 5 folders:&nbsp;</p> <p>K1, T2, M3 and M4 contain the raw data collected by active acoustic monitoring system and various pumps and transducers.&nbsp;<br> The readings of the Top Industrie syringe pump (for fluid injection), pressure transducers at downstream, and GDS pumps that provide confining stresses along all three directions via flatjacks are provided by two excel spreadsheets - Low_frequency_measurements.csv and Pump_reading.csv.<br> For active acoustic data, there are four different files named by the starting time for each experiment. The .json file contains the basic information of each experiment. The .txt file contains the acquisition time for each active acoustic sequence. The .bin file contains the collected waveforms of all acoustic sequences.</p> <p>Processed_data includes the synchronized pressure data (Pressure_data.xlsx) and detailed acoustic emission results (AE_K1.csv, AE_T2.csv, AE_M3.csv, AE_M4.csv).<br> &nbsp;</p>

opencc-by-4.0Oct 2023View details →
zenodo44/100

Data part of the manuscript Anaerobic methanotrophy is stimulated by graphene oxide in a brackish urban canal sediment

<p>We surveyed three canals in the city of Amsterdam (Netherlands) for it methane emissions and potential to filter methane through anaerobic oxidation of methane in the canal sediment. To unravel the mechanisms involved we characterised the sediment geochemically. All data present in the manuscript is available in the Excel file.</p>

opencc-by-4.0Dec 2022View details →
zenodo44/100

Datasets used for the manuscript: "Sibling competition, dispersal and fitness outcomes in humans"

<p>Datasets used for the manuscript: &ldquo;Sibling competition, dispersal and fitness outcomes in humans&rdquo;, 10.1038/s41598-023-33700-3</p>

opencc-by-4.0Apr 2023View details →
zenodo44/100

Data for the study of Posidonia microbial nitrogen metabolism manuscript

<p>These are data related to the study of the seagrass microbiome and function. <em>Posidonia oceanica</em>, an endemic seagrass species that dominates the Mediterranean Sea, achieves high abundances in seawater with relatively low concentrations of dissolved inorganic nitrogen. Here we test whether microbial metabolisms associated with <em>P. oceanica</em> and surrounding seawater enhance seagrass access to nitrogen. Using stable isotope enrichments of intact seagrass with amino acids, we show that ammonification by free-living and seagrass-associated microbes produce ammonium that is likely used by seagrass and surrounding particulate organic matter. Metagenomic analysis of the epiphytic biofilm on the blades and rhizomes support the ubiquity of microbial ammonification genes in this system. Further, we leveraged the presence of natural carbon dioxide vents and show that microbial ammonification was reduced at lower pH. The presence of <em>P. oceanica</em> enhanced the uptake of nitrogen by water column particulate organic matter, increasing carbon fixation by a factor of 8.6 to 17.4 with the greatest effect at CO<sub>2</sub> vent sites. Seagrass and its microbial associates thus enhanced water column productivity and were a locus for nutrient cycling.</p>

opencc-by-4.0May 2023View details →
zenodo44/100

Supplementary Material of the Manuscript: "The effects of blank size and knapping strategy on the estimation of core's reduction intensity"

<p>This repository hosts the R-markdown&nbsp;and dataset&nbsp;that allow reproducibility and replicability of the statistical analyses implemented in the paper: Lombao, D., Cueva-Temprana, A., Rabu&ntilde;al, J.R., Morales, J.I., Mosquera, M.&nbsp;&nbsp;The effects of blank size and knapping strategy on the estimation of core&rsquo;s reduction intensity.&nbsp;<em>Archaeol Anthropol Sci</em>&nbsp;<strong>11</strong>, 5445&ndash;5461 (2019). https://doi.org/10.1007/s12520-019-00879-4<br> For further information, please open first&nbsp;the readme.txt. document.</p>

opencc-by-4.0May 2023View details →
zenodo44/100

Supporting data for manuscript "Chemical and visual characterisation of EGRIP glacial ice and cloudy bands within "

<p>Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) offers micron-resolution 2D chemical imaging, which has been adapted recently to ice core analysis. The datasets are supporting information for the manuscript &quot;Chemical and visual characterisation of EGRIP glacial ice and cloudy bands within&quot; accepted for publication in &quot;The Cryosphere&quot; (https://doi.org/10.5194/tc-2022-250). Measurements were performed at the Ca&rsquo;Foscari University of Venice, considered as analytes are 23Na, 24Mg, 27Al, 48Ti, 56Fe and 88Sr. Background and drift correction as well as image construction were performed using the software HDIP (Teledyne Photon Machines, Bozeman, MT, USA). Impurity maps are acquired as a pattern of lines, without overlap in the direction perpendicular to that of the scan, and without any further spatial interpolation. For each of the maps, for every chemical channel the intensities (in counts, after background and drift correction) are provided as a separate file. These maps were obtained using a 20 &micro;m square spot. Samples are referred to using the original identifier of the manuscript, e.g. S2 for sample 2 from 1367.05 m depth.</p>

opencc-by-4.0May 2023View details →
zenodo44/100

Supplementary datasets for the manuscript "Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states" - Part 2

<p>Supplementary files containing datasets needed to reproduce the results of the manuscript &quot;Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states&quot; by S. Choudhury et al.</p> <p>The code to use with these data and reproduce the manuscript results is available at&nbsp; https://github.com/EPFL-LCSB/renaissance and https://gitlab.com/EPFL-LCSB/renaissance. The execution of parts of this code is dependent on the SkimPy toolbox (https://github.com/EPFL-LCSB/skimpy). Refer to the readme files on the RENAISSANCE code repositories for more details.</p> <p>The dataset contains the following files:</p> <p>1. param_fixing.zip - self-explanatory (Figure 4 &amp; 5); contains an explanatory note for this part (experiment_details.txt), and the file containing Km values fetched from the BRENDA database (Km_database.csv).</p> <p>2. scripts.zip - scripts to generate figure 2-5 on toy data</p>

opencc-by-4.0May 2023View details →
zenodo44/100

Supplementary datasets for the manuscript "Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states" - Part 1

<p><strong>Supplementary files containing datasets needed to reproduce the results of the manuscript "Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states" by S. Choudhury et al (https://doi.org/10.1101/2023.02.21.529387).</strong></p> <p>The code to use with these data and reproduce the manuscript results is available at&nbsp; https://github.com/EPFL-LCSB/renaissance and https://gitlab.com/EPFL-LCSB/renaissance. The execution of parts of this code is dependent on the SkimPy toolbox (https://github.com/EPFL-LCSB/skimpy). Refer to the readme files on the RENAISSANCE code repositories for more details.</p> <p>The dataset contains the following files:</p> <p>1. models.zip - contains thermodynamically curated steady-state and nonlinear kinetic models of <em>E. coli </em>metabolism used in this study. Also contains the samples of steady-state metabolite concentrations and metabolic fluxes used in the study presented in Figure 3 (steady-state samples used for preparing Figures 2 and 4).</p> <p>2. renaissance_incidence_results.zip - self-explanatory (Figure 2a and 2b)</p> <p>3. ODE_solutions.zip - self-explanatory (Figure 2c)</p> <p>4. bioreactor_simulations1-3.zip - self-explanatory (Figure 2d)</p> <p>5. steady_state_analysis.zip - RENAISSANCE results obtained for each of the steady states (Figure 3a)</p> <p>6. subspace_analysis.zip - RENAISSANCE results presented in Figure 3b-g</p> <p><strong>The remaining datasets are published in the following links</strong></p> <p><em>&nbsp;- https://doi.org/10.5281/zenodo.7930084</em></p> <p><em>&nbsp;- https://doi.org/10.5281/zenodo.10391802</em></p>

opencc-by-4.0Feb 2023View details →
zenodo44/100

Data tables associated with manuscript 'Grant et al., Regional amplified warming in the Southwest Pacific during the mid-Pliocene (3.3-3.0 Ma)'

<p>This repository holds the data files associated with manuscript Grant et al.,&nbsp;&nbsp;Regional amplified warming in the Southwest Pacific during the mid-Pliocene (3.3-3.0 Ma), submitted to Climate of the Past.&nbsp;https://doi.org/10.5194/egusphere-2023-108&nbsp;</p> <p>&nbsp;&nbsp;The R Script&nbsp;and R Data used to analyse the data and produce the figures can be&nbsp;found in GitHub repository https://github.com/GRG-GNS/Pliocene-SST-Southwest-Pacific.git</p> <p>###########Terms and units</p> <p>Sea Surface Temperatures (SSTs) are in degrees Celsius. Latitude are in degrees north. Longitude in degrees east.</p> <p>&nbsp;</p> <p>NZESM (New Zealand Earth system model; Williams et al., 2016), UKESM (United Kingdom Earth System model; Sellar et al., 2019), &nbsp;HadISST 1870-1879 AD (HadleyCentre Sea Ice and Sea Surface Temperature; NCAR, 2022), mPWP (mid-Pliocene Warm Period 3.3 - 3.0 Ma),&nbsp;MIS5e (Marine Isotope Stage 5e; 125 ka). SSP1 /2/ 3 (Socio-economic Pathways; IPCC). UK&#39;37 - alkenone biomarker SST proxy TEX - TEX86 biomarker SST proxy</p> <p>Two periods&nbsp;were extracted from NZESM and UKESM i) 2036-2040 AD for SSP 2, and ii) 2090-2099 AD for SSP1, SSP 2, SSP 3. These are provided as stand alone values and in reference to HadiIST (e.g. NZESM - HadISST or NZESM.HadISST)&nbsp;</p> <p><strong>Table 2.</strong>&nbsp;<strong>Statistical distribution of mid-Pliocene Warm Period (3.3-3.0 Ma) Sea Surface Temperatures anomalies (SST; &deg;C) relative to HadiSST (1870-1879 AD) using </strong> <strong>BAYSPLINE calibration (Tierney and Tingley, 2018).&nbsp; The total range is calculated as the difference between maximum and minimum temperature and represents glacial to interglacial extremes. </strong></p> <p><strong>Table 3. Site annual mean Sea Surface Temperature anomalies (SST; &deg;C) for UKESM and NZESM with respect to HadISST (1870-1879 AD) for SSP2-4.5 2040 AD (2036&ndash;2045 AD).&nbsp;&nbsp;</strong></p> <p><strong>Table 4. Site annual mean Sea Surface Temperature anomalies (SST; &deg;C)for UKESM and NZESM with respect to HadISST (1870-1879 AD)&nbsp;for SSP1-2.6, SSP2-4.5, SSP3-7.0 at 2095 AD (2090&ndash;2099 AD).&nbsp;&nbsp;</strong></p> <p><strong>Table A1.&nbsp;Comparison between </strong> <strong>&nbsp;derived SST using BAYSPLINE with TEX<sub>86</sub>&nbsp;-index SST calibrations of Schouten <em>et al</em>. (2002), Kim <em>et al</em>, (2010), OPTIMAL (Dunkley Jones <em>et al</em>.,&nbsp;2020) and BAYSPAR (Tierney and Tingley, 2015). </strong></p> <p><strong>Table S1. All site sea surface temperature (SST; &deg;C) data used in results with &nbsp;index and calibrations of M&uuml;ller98 (M&uuml;ller <em>et al</em>., 1998) and BAYSPLINE (Tierney and Tingley, 2018). The proxy type and references are also provided.</strong></p> <p><strong>Table S2. Site sample data for analyses undertaken this study, including all &nbsp;and TEX<sub>86 </sub>index calculations and calibrations. References for calibrations are contained within column headers.</strong></p> <p><strong>Table S3. Seasonal and annual mean sea surface temperature (SST; &deg;C) model outputs of HadISST (NCAR, 2022), UKESM (Sellar <em>et al</em>., 2019), NZESM (Williams <em>et al</em>., 2016) at the seven Southwest Pacific sites (DSDP 594, ODP 1172, ODP 1168, ODP 1125, ODP 1123, DSDP 593, DSDP 590) for SSP2 2040 AD (2036-2045 AD), and SSP1, 2, and 3 2095 AD (2090-2099 AD). Including UKESM and NZESM with respect to HadISST.</strong></p> <p><strong>Table S4. Site sea surface temperature (SST; &deg;C) annual means and seasonal range for UKESM and NZESM SSP2-4.5 2036-2045 AD, with MPWP interglacial modal means and total glacial range (maximum to minimum SST). &nbsp;</strong></p> <p><strong>Table S5. Compiled sea surface temperature (SST; &deg;C) interglacial means for MIS 5e (125kyr; Cortese et al., 2013) and mPWP (3.3-3.0 Ma) and model annual means for HadISST (1870-1879 AD), and SSP2-4.5 2090-2099 AD for UKESM, NZESM.</strong></p> <p>&nbsp;</p>

opencc-by-4.0Sep 2022View details →
zenodo44/100

Source data for manuscript "Real-time microscopy of the relaxation of a glass".

<p>Source data for manuscript &quot;Real-time microscopy of the relaxation of a glass&quot; (DOI: 10.1038/s41567-023-02125-0), including:</p> <p>- AFM source images</p> <p>- data points for all plots in the manuscript</p>

opencc-by-4.0Dec 2022View details →

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